A method to quantify the influence of kinetically modelled biogeochemical processes on the pH of an ecosystem with time variable acid-base dissociation constants is presented and applied to the heterotrophic, turbid Scheldt estuary (SW Netherlands, N Belgium). Nitrification is identified as the main process governing the pH profile of this ... read more estuary, while CO2 degassing and advective-dispersive transport "buffer" the effect of nitrification. CO2 degassing accounts for the largest proton turnover per year in the whole estuary. There is a clear inverse correlation between oxygen turnover and proton turnover. The main driver of long-term changes in the mean estuarine pH from 2001 to 2004 is a changing freshwater flow which influences the pH "directly" via [∑CO2] and [TA] and to a significant amount also "indirectly" via [∑NH4+] and the nitrification rates in the estuary. show less